The complex architecture of plant transgene insertions

Jupe, Florian; Tp, Michael; Ac, Rivkin; Zander, Mark; S, Timothy Motley; Jp, Sandoval; R, Keith Slotkin; Chen, H; Castagnon, R; Nery, Joseph R.; Ecker,

doi:10.1101/282772

Cited by 3 publications

(3 citation statements)

References 55 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The integration of Agrobacterium transfer DNA (T-DNA) occurs at existing double strand breaks through the activity of native polymerase theta and microhomology-mediated repair (van Kregten et al, 2016). Despite its relative precision, most T-DNA insertions are at least dimers (van Kregten et al, 2016) and many are composed of long arrayed multimers (Cluster et al, 1996;Krizkova and Hrouda, 1998;Jupe et al, 2018). In addition, Agrobacterium transformation may result in multiple T-DNA insertions at different locations, large deletions (Takano et al, 1997;Kaya et al, 2000), chromosomal inversions, translocations, and duplications (Takano et al, 1997;Nacry et al, 1998;Clark and Krysan, 2010;Zhu et al, 2010;Anderson et al, 2016;Jupe et al, 2018).…”

Section: Introductionmentioning

confidence: 99%

Genome-Scale Sequence Disruption Following Biolistic Transformation in Rice and Maize

et al. 2019

View full text Add to dashboard Cite

Biolistic transformation delivers nucleic acids into plant cells by bombarding the cells with microprojectiles, which are micron-scale, typically gold particles. Despite the wide use of this technique, little is known about its effect on the cell's genome. We biolistically transformed linear 48-kb phage lambda and two different circular plasmids into rice (Oryza sativa) and maize (Zea mays) and analyzed the results by whole genome sequencing and optical mapping. Although some transgenic events showed simple insertions, others showed extreme genome damage in the form of chromosome truncations, large deletions, partial trisomy, and evidence of chromothripsis and breakage-fusion bridge cycling. Several transgenic events contained megabase-scale arrays of introduced DNA mixed with genomic fragments assembled by nonhomologous or microhomology-mediated joining. Damaged regions of the genome, assayed by the presence of small fragments displaced elsewhere, were often repaired without a trace, presumably by homology-dependent repair (HDR). The results suggest a model whereby successful biolistic transformation relies on a combination of end joining to insert foreign DNA and HDR to repair collateral damage caused by the microprojectiles. The differing levels of genome damage observed among transgenic events may reflect the stage of the cell cycle and the availability of templates for HDR.

show abstract

Section: Introductionmentioning

confidence: 99%

Genome-Scale Sequence Disruption Following Biolistic Transformation in Rice and Maize

et al. 2019

View full text Add to dashboard Cite

show abstract

“…The integration of Agrobacterium transfer DNA (T-DNA) occurs at spurious double strand breaks through the activity of native polymerase theta and microhomology-mediated repair 3 . Despite its relative precision, most T-DNA insertions are at least dimers 3 and many are composed of long arrayed multimers [4][5][6] . In addition, Agrobacterium transformation may result in multiple T-DNA insertions across the genome, and integration can result in large deletions 7,8 as well as chromosomal inversions, translocations, and duplications 4,[8][9][10][11][12] .…”

Section: Introductionmentioning

confidence: 99%

Genome-scale sequence disruption following biolistic transformation in rice and maize

Liu¹,

Nannas

Fu³

et al. 2018

Preprint

View full text Add to dashboard Cite

We biolistically transformed linear 48 kb phage lambda and two different circular plasmids into rice and maize and analyzed the results by whole genome sequencing and optical mapping.While some transgenic events showed simple insertions, others showed extreme genome damage in the form of chromosome truncations, large deletions, partial trisomy, and evidence of chromothripsis and breakage-fusion bridge cycling. Several transgenic events contained megabase-scale arrays of introduced DNA mixed with genomic fragments assembled by non-homologous or microhomology-mediated joining. Damaged regions of the genome, assayed by the presence of small fragments displaced elsewhere, were often repaired without a trace, presumably by homology-dependent repair (HDR). The results suggest a model whereby successful biolistic transformation relies on a combination of end joining to insert foreign DNA and HDR to repair collateral damage caused by the microprojectiles. The differing levels of genome damage observed among transgenic events may reflect the stage of the cell cycle and the availability of templates for HDR.

show abstract

“…RNA-seq of one of the transgenic lines (CENH3-Ox-1 ) showed approximately four-fold higher expression of the transgene than the wild type copy of CENH3 (Figure 6B). Quantitative PCR analysis of genomic DNA from the CENH3-Ox-1 line suggested that the high CENH3 expression in this line is caused by multiple transgene insertions (Figure 6B), which is a frequent occurrence in Agrobacterium transformants (Shou et al 2004; Jupe et al 2018). These four transgenes are sufficient to fully complement the cenh3 null mutation (Wang et al, in press ).…”

Section: Resultsmentioning

confidence: 99%

Maize centromeric chromatin scales with changes in genome size

Wang

Liu

Ricci

et al. 2020

Preprint

View full text Add to dashboard Cite

Centromeres are defined by the location of Centromeric Histone H3 (CENP-A/CENH3) which interacts with DNA to define the locations and sizes of functional centromeres. An analysis of 26 maize genomes including 110 fully assembled centromeric regions revealed positive relationships between centromere size and genome size. These effects are independent of variation in the amounts of the major centromeric satellite sequence CentC. We also backcrossed known centromeres into two different lines with larger genomes and observed consistent increases in functional centromere sizes for multiple centromeres. Although changes in centromere size involve changes in bound CENH3, we could not mimic the effect by overexpressing CENH3 by threefold. Literature from other fields demonstrate that changes in genome size affect protein levels, organelle size and cell size. Our data demonstrate that centromere size is among these scalable features, and that multiple limiting factors together contribute to a stable centromere size equilibrium.

show abstract

The complex architecture of plant transgene insertions

Cited by 3 publications

References 55 publications

Genome-Scale Sequence Disruption Following Biolistic Transformation in Rice and Maize

Genome-Scale Sequence Disruption Following Biolistic Transformation in Rice and Maize

Genome-scale sequence disruption following biolistic transformation in rice and maize

Maize centromeric chromatin scales with changes in genome size

Contact Info

Product

Resources

About